Hi Mustafa,
On 8/07/2011, at 4:02 AM, MUSTAFA BUGHIO wrote:
> Thanks beb
>
> I am new user of AMBER, i have given input file named min500res.in for
> minimization of my protein. Its pentamer homology model which i have
> neutralised by adding charges and solvated in TIP3PBOX 10A. Yes you are
> right that it should be minimized before MD run that's what i am trying to
> do but following error is reported.
>
> Other than AMBER minimization i tried to minimize via Sybyl and Modeller
> optimization program. I found that after minimization my proteins Beta
> sheets were completely disappeared and formed all loops. But when i
> minimized only Monomer by same input file it had removed bad clashes and my
> PDB was better refined therefore i am trying to repeat same procedure with
> pentamer which gives VDWAALS error.
I trust that you've ensured your monomers (in the pentamer) aren't superimposed.
> Is there any process to minimize VDW forces other than AMBER. If giving
> cutoff value can help me. as i have not given any cutoff in my input file.
Please provide your input file. The cutoff is probably not an issue in this case.
A default value for the cutoff will be used if it's not explicitly set.
Regards,
Ben
--
For greater security, I support S/MIME encryption.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/pkcs7-signature attachment: smime.p7s
Received on Fri Jul 08 2011 - 05:00:03 PDT
